Create ligand list

Information

Create a list of protein structures containing specialized ligands. The resulting list contains information about the location of the ligand in the structure files (pdbID, chain, residueID).

Create list of protein structures containing ligand subsets

Search Objective: Distinct ligands		Insert one or more ligands (comma seperated). Entering more than one Ligand leads to all Structures containing one of the chosen Ligands.
Similarity to Ligand		Insert a ligand's HetId for selecting a set of ligands beeing simmilar to this compound
Similarity to Drug		Insert a drug's CasId for selecting a set of ligands beeing simmilar to this compound
Similarity level:		Minimal Tanimoto used for creation of ligand lists (not more than 10 differnt ligands are choosen due to performance)
Trend to lie in pockets:		Upper border for Ligand validation. Ligands without validation are added allways.
Binding State:	Unbound  Bound to protein  Bound to ligand  Part of polypeptide  Part of polynucleotide	Check binding states which are allowed for the ligands. Leave all unchecked to ignore this selection.
Create cluster based on:	No Cluster Blastc 95% Blastc 90% Blastc 70% Blastc 50% Blastc 40% Blastc 30% cdHit 95% cdHit 90% cdHit 70% cdHit 50%	Select clustering which should be done on the resulting protein structures.

Note: For an automated generation of protein lists check out our documentation.